The UN Stabilisation Mission in Haiti (MINUSTAH) said Da Matta Bacellar's body had been found on Saturday morning in his room at the Hotel Montana, and he had been shot.
The report said he appeared to have committed suicide.
Chilean General Eduardo Aldunate Herman will take over as interim military commander of the mission in Haiti, defence ministry officials said.
The UN mission expressed sorrow and said in a statement that Da Matta Bacellar's "tragic death" was being investigated.
"His untimely death and sacrifice in the cause of peace will not weaken the resolve of MINUSTAH and the international community to ensure the will of the Haitian people prevails and Haiti joins the democratic community of nations," the UN mission said.
The death of the UN commander comes as United Nations forces and the Haitian authorities struggle to maintain order amid growing unrest and a wave of kidnappings in the capital.
The UN mission has come under sharp criticism in recent days, with political parties accusing the peacekeepers of "passivity and tolerance" as armed groups run amok.
The country has been unstable
since Aristide was ousted
Violence and kidnappings have plagued the impoverished Caribbean nation since former president Jean Bertrand Aristide fled on 29 February 2004 as rebels closed in on the capital.
The first presidential elections since Aristide was forced from office were supposed to be held months ago but have been repeatedly postponed, partly due to the precarious security conditions.
The vote, most recently scheduled for 8 January, has been delayed for a fourth time, with government preparations mired in disarray.
Many of the 3.5 million registered voters have yet to receive their electoral identification cards, while officials have yet to determine the location of the 800 voting offices and the make-up of electoral observer teams.
On Friday, the UN Security Council called on Haiti's interim government to hold the presidential polls as soon as possible and no later than 7 February.
Da Matta Bacellar took over the UN post on 31 August, commanding 7500 military personnel from 14 different countries.
Brazil has the largest contingent in MINUSTAH, with 1213 troops, followed by Nepal, Jordan and Sri Lanka, with 750 each.